Let's get redbiom-ing #2118

antgonza · 2017-04-26T15:19:15Z

Just installing redbiom, once the test pass I'll add a handler

…m-ing

…om-ing

coveralls · 2017-05-07T17:00:42Z

Coverage increased (+0.0003%) to 91.976% when pulling 9bd1166 on antgonza:redbiom-ing into eb8863b on biocore:redbiom.

antgonza · 2017-05-07T17:09:11Z

I think this is ready for review. Sorry for the amount of changes but as you can imagine, had to do a bunch of tests/changes based on these. Note that this goes to it's own branch so it should be fine to merge once is reviewed and changes are approved.

At this point, we are using redbiom to only get the sample_ids that match a giving query (metadata or sequence), to then use the database to find the artifacts (based on the preparations) and their information where those samples exist.

The ToDo list is as follows, this list will be moved to the PR against master once this one is merged:

Move out database code from qiita_pet.handler
Decide what to do with the context limitation to search based on sequences. Let's discuss this on our next Qiita meeting.
Decide what to do with displaying on which categories/artifacts the search query is found. Also, let's discuss on next Qiita meeting.
Fix GUI based on decisions on the last points.
Others??

coveralls · 2017-05-07T18:25:24Z

Coverage decreased (-0.009%) to 91.967% when pulling 28a9902 on antgonza:redbiom-ing into eb8863b on biocore:redbiom.

coveralls · 2017-05-07T20:39:17Z

Coverage decreased (-0.009%) to 91.967% when pulling 17e0780 on antgonza:redbiom-ing into eb8863b on biocore:redbiom.

wasade · 2017-05-09T04:31:53Z

qiita_pet/handlers/qiita_redbiom.py

+    @coroutine
+    @execute_as_transaction
+    def get(self, search):
+        contexts = yield Task(self._get_context)


just curious, how annoying was it to deal with these Tasks?

Once you get the drift, pretty easy.

wasade · 2017-05-09T04:32:57Z

qiita_pet/handlers/qiita_redbiom.py

+            callback(([], 'The given context is not valid: %s - %s' % (
+                context, contexts)))
+        else:
+            if search_on == 'metadata':


we may want an additional elif here for searching over categories

yup, let's chat this afternoon

wasade · 2017-05-09T04:33:22Z

qiita_pet/handlers/qiita_redbiom.py

+                context, contexts)))
+        else:
+            if search_on == 'metadata':
+                samples = redbiom.search.metadata_full(query, categories=None)


categories is defined as a bool, can this be set to categories=False?

wasade · 2017-05-09T04:35:49Z

qiita_pet/handlers/qiita_redbiom.py

+            if search_on == 'metadata':
+                samples = redbiom.search.metadata_full(query, categories=None)
+            elif search_on == 'observations':
+                # from_or_nargs first parameter is the file handler so it uses


I don't understand this comment. from_or_nargs handles the case of passing in a list of things via a file or from the command line

in one of the previous versions I was using from_or_nargs but then replaced with current code and forgot to remove that comment, removing.

wasade · 2017-05-09T04:36:38Z

qiita_pet/handlers/qiita_redbiom.py

+                # the values from query
+                samples = [s.split('_', 1)[1]
+                           for s in redbiom.util.samples_from_observations(
+                               query.split(' '), True, context)]


the True here may not be always desirable but that can be deferred

yup, also within our discussion today.

wasade · 2017-05-09T04:39:07Z

qiita_pet/handlers/qiita_redbiom.py

+                # from_or_nargs first parameter is the file handler so it uses
+                # that as the query input. None basically will force to take
+                # the values from query
+                samples = [s.split('_', 1)[1]


What this is doing is converting from a redbiom ID to an ambiguous ID, and it does not seem to be enforcing that the ID is unique through a set comprehension. You may want to use redbiom.util.resolve_ambiguities instead

ok, this is one of the other things we should discuss this afternoon.

wasade · 2017-05-09T04:39:41Z

qiita_pet/handlers/qiita_redbiom.py

+                callback(([], 'Incorrect search by: you can use observations '
+                          'or metadata and you passed: %s' % search_on))
+
+            if bool(samples):


why cast to bool?

I read somewhere that was the safest way to test for an empty set ...

wasade · 2017-05-09T04:41:05Z

qiita_pet/static/js/qiita.js

@@ -117,3 +117,90 @@ function show_hide_process_list() {
    $("#qiita-processing").hide();
  }
 }
+


i may not be the best person for review of changes to this file

it's mainly moving code around so the libraries are available everywhere vs. just in the study listing

Can you add documentation to the JavaScript functions? I know at the beginning we were not doing it but I started doing it based on the Emperor documentation and it is really useful (i.e. it serves the same goal as the numpy doc).

tried to add as many as possible

wasade · 2017-05-09T04:41:55Z

qiita_pet/templates/redbiom.html

+        // render Artifact Processing
+        {"render": function ( data, type, row, meta ) {
+            var text = '';
+            if (!(!row.command)) {


Isn't a double negative a positive?

yup, again read somewhere that to test is a variable is not undefined or null the easiest is to do !row.command but didn't want to add an else so just negated that boolean ...

wasade · 2017-05-09T04:45:06Z

qiita_pet/handlers/qiita_redbiom.py

+    @execute_as_transaction
+    def _redbiom_search(self, context, query, search_on, callback):
+        df = redbiom.summarize.contexts()
+        contexts = df.ContextName.values


per gchat, we may want to filter these. And one other possibility in addition to what we discussed was is to filter on load of the cache as well.

yup, let's chat this afternoon

antgonza

thanks for reviewing, this should make our conversation go faster this afternoon and we are getting closer

antgonza · 2017-05-09T12:14:42Z

INSTALL.md

@@ -87,6 +88,26 @@ brew update
 brew install homebrew/versions/redis28
 ```

+### webdis
+
+Note that this is the only package that assumes that Qiita is already installed (due to library dependencies). Also, that the general suggestion is to have 2 redis servers running, one for webdis/redbiom and the other for Qiita. The default configuration has webdis/redbiom running on the default redis port and Qiita's on 7777.


antgonza · 2017-05-09T12:15:49Z

INSTALL.md

@@ -163,6 +184,12 @@ Next, make a test environment:
 qiita-env make --no-load-ontologies
 ```

+Finally, redbiom rely on the REDBIOM_HOST environment variable to set the URL to query. By default is set to http://127.0.0.1:7379, which is the webdis default. For example you could:


k, makes sense for default installations but it might be better to leave as is as the idea of these instructions is to have local installations for development.

antgonza · 2017-05-09T12:16:19Z

qiita_pet/handlers/qiita_redbiom.py

+    @coroutine
+    @execute_as_transaction
+    def get(self, search):
+        contexts = yield Task(self._get_context)


Once you get the drift, pretty easy.

antgonza · 2017-05-09T12:16:58Z

qiita_pet/handlers/qiita_redbiom.py

+    @execute_as_transaction
+    def _redbiom_search(self, context, query, search_on, callback):
+        df = redbiom.summarize.contexts()
+        contexts = df.ContextName.values


yup, let's chat this afternoon

antgonza · 2017-05-09T12:17:14Z

qiita_pet/handlers/qiita_redbiom.py

+            callback(([], 'The given context is not valid: %s - %s' % (
+                context, contexts)))
+        else:
+            if search_on == 'metadata':


yup, let's chat this afternoon

antgonza · 2017-05-09T12:19:17Z

qiita_pet/handlers/qiita_redbiom.py

+                # from_or_nargs first parameter is the file handler so it uses
+                # that as the query input. None basically will force to take
+                # the values from query
+                samples = [s.split('_', 1)[1]


ok, this is one of the other things we should discuss this afternoon.

antgonza · 2017-05-09T12:19:40Z

qiita_pet/handlers/qiita_redbiom.py

+                # the values from query
+                samples = [s.split('_', 1)[1]
+                           for s in redbiom.util.samples_from_observations(
+                               query.split(' '), True, context)]


yup, also within our discussion today.

antgonza · 2017-05-09T12:32:13Z

qiita_pet/handlers/qiita_redbiom.py

+                callback(([], 'Incorrect search by: you can use observations '
+                          'or metadata and you passed: %s' % search_on))
+
+            if bool(samples):


I read somewhere that was the safest way to test for an empty set ...

antgonza · 2017-05-09T12:33:07Z

qiita_pet/static/js/qiita.js

@@ -117,3 +117,90 @@ function show_hide_process_list() {
    $("#qiita-processing").hide();
  }
 }
+


it's mainly moving code around so the libraries are available everywhere vs. just in the study listing

antgonza · 2017-05-09T12:34:08Z

qiita_pet/templates/redbiom.html

+        // render Artifact Processing
+        {"render": function ( data, type, row, meta ) {
+            var text = '';
+            if (!(!row.command)) {


yup, again read somewhere that to test is a variable is not undefined or null the easiest is to do !row.command but didn't want to add an else so just negated that boolean ...

coveralls · 2017-05-10T14:51:39Z

Coverage decreased (-0.02%) to 91.955% when pulling d46392e on antgonza:redbiom-ing into eb8863b on biocore:redbiom.

josenavas

A few comments.

josenavas · 2017-05-10T22:22:40Z

.travis.yml

+  # first let's make sure redis is empty
+  - curl -s http://127.0.0.1:7379/FLUSHALL > /dev/null
+  - redbiom admin create-context --name "qiita-test" --description "qiita-test context"
+  - fp=`python -c 'import qiita_db; print qiita_db.__file__'`


I think this line and the one below can be removed. Then instead of using ${qdbd} on the other lines you can simply use `pwd`/qiita_db/. According to lines 40, 42, and 43 that should work w/o a problem

josenavas · 2017-05-10T22:23:39Z

INSTALL.md

@@ -60,6 +60,7 @@ Install the non-python dependencies

 * [PostgreSQL](http://www.postgresql.org/download/) (minimum required version 9.3.5, we have tested most extensively with 9.3.6)
 * [redis-server](http://redis.io) (we have tested most extensively with 2.8.17)
+* [webdis] (https://github.com/nicolasff/webdis) (latest version should be fine)


Can you make a comment similar to the one in redis? i.e. Latest version should be fine but we have tested most extensively with XXXX.

josenavas · 2017-05-10T22:24:11Z

INSTALL.md

@@ -87,6 +88,26 @@ brew update
 brew install homebrew/versions/redis28
 ```

+### webdis
+
+Note that this is the only package that assumes that Qiita is already installed (due to library dependencies). Also, that the general suggestion is to have 2 redis servers running, one for webdis/redbiom and the other for Qiita. The default configuration. The reason for multiple redis servers is so that the redbiom cache can be flushed without impacting the operation of the qiita server itself.


Remove The default configuration or complete the sentence.

josenavas · 2017-05-10T22:26:13Z

INSTALL.md

+make
+./webdis &
+popd
+wget https://raw.githubusercontent.com/wasade/redbiom/master/Makefile


The instructions outlined here looks like they're for setting up a test environment, but I don't believe that is the goal of this documentation. I think it should list the commands used to generate the release from Qiita, populate the redbiom DB from that file and then how to set up a job so that the cache gets updated periodically.

yup, this is a copy of the first version with loaded the redbiom db; the new one actually loads the qiita data so changing

josenavas · 2017-05-10T22:26:47Z

qiita_pet/handlers/qiita_redbiom.py

@@ -0,0 +1,163 @@
+from tornado.gen import coroutine, Task


This file is missing the copyright header.

josenavas · 2017-05-10T23:03:02Z

qiita_pet/test/test_qiita_redbiom.py

@@ -0,0 +1,161 @@
+from unittest import main


This file is missing the copyright notice

josenavas · 2017-05-10T23:03:48Z

qiita_pet/test/test_qiita_redbiom.py

+        response = self.post('/redbiom/', post_args)
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success',
+               'message': ('Not a valid search: "4353076", are you sure this '


Why is this not a valid metadata value?

cause it's not a stem ...

not exactly. we intentionally do not index things which look like numbers as i could not determine a reasonable strategy for determining when a number was or was not a good thing to index. in general, it is not and it would have very large impact on the key space. however, as a downside, important numbers like host taxon ID are not index. but, if a user knows they want to search for host taxon ID, they can still do that with where host_taxid=foo

OK, thanks for the explanation. I'll coordinate with you to write some of these explanations and add them to the instructions.

josenavas · 2017-05-10T23:05:06Z

qiita_pet/test/test_qiita_redbiom.py

+
+    def test_post_observations(self):
+        post_args = {
+            'search': ('4479944'),


Not sure why these values are in parenthesis? They are not needed. (Applies to all)

you are right but they don't hurt or aren't flake8 complaint ... so?

josenavas · 2017-05-10T23:05:39Z

qiita_pet/test/test_qiita_redbiom.py

+        response = self.post('/redbiom/', post_args)
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success',
+               'message': ('Not a valid search: "4353076", are you sure this '


Same question as above - why it is not valid?

also not a stem ... I guess that it will become valid if a metadata category or value is 4353076, @wasade?

In order to allow this to move forward, can this be added as a TODO item (even if it is only a discussion)? I don't understand why a number will not be a valid stem, or why searching over numerical values is not allowed. However, I don't want to block this PR for this discussion.

k, will do, now numerical values are fine but have to be inclosed in a where, like where age_cat > 40

@josenavas, that would mean we'd index every single pH value, elevation, lat/long, etc in the absence of context.

Thanks for the explanation @wasade , that makes sense.

josenavas · 2017-05-10T23:07:04Z

scripts/qiita-test-install

@@ -395,6 +430,8 @@ def main():
        ipython_running = False
        extra_info = ('IPython test failed, perhaps due to an old MOI '
                      'version, please review')
+
+    print qiita_config_header


Remove print?

it's actually needed so it's displayed, see line https://github.com/biocore/qiita/pull/2118/files#diff-bb7154348182dace785aedbad03c3a2bL341

antgonza

thanks

antgonza · 2017-05-11T11:50:00Z

.travis.yml

+  # first let's make sure redis is empty
+  - curl -s http://127.0.0.1:7379/FLUSHALL > /dev/null
+  - redbiom admin create-context --name "qiita-test" --description "qiita-test context"
+  - fp=`python -c 'import qiita_db; print qiita_db.__file__'`


antgonza · 2017-05-11T11:50:08Z

INSTALL.md

@@ -60,6 +60,7 @@ Install the non-python dependencies

 * [PostgreSQL](http://www.postgresql.org/download/) (minimum required version 9.3.5, we have tested most extensively with 9.3.6)
 * [redis-server](http://redis.io) (we have tested most extensively with 2.8.17)
+* [webdis] (https://github.com/nicolasff/webdis) (latest version should be fine)


antgonza · 2017-05-11T11:50:14Z

INSTALL.md

@@ -87,6 +88,26 @@ brew update
 brew install homebrew/versions/redis28
 ```

+### webdis
+
+Note that this is the only package that assumes that Qiita is already installed (due to library dependencies). Also, that the general suggestion is to have 2 redis servers running, one for webdis/redbiom and the other for Qiita. The default configuration. The reason for multiple redis servers is so that the redbiom cache can be flushed without impacting the operation of the qiita server itself.


antgonza · 2017-05-11T11:51:09Z

INSTALL.md

+make
+./webdis &
+popd
+wget https://raw.githubusercontent.com/wasade/redbiom/master/Makefile


yup, this is a copy of the first version with loaded the redbiom db; the new one actually loads the qiita data so changing

antgonza · 2017-05-11T11:51:15Z

qiita_pet/handlers/qiita_redbiom.py

@@ -0,0 +1,163 @@
+from tornado.gen import coroutine, Task


antgonza · 2017-05-11T13:16:19Z

qiita_pet/test/test_qiita_redbiom.py

@@ -0,0 +1,161 @@
+from unittest import main


antgonza · 2017-05-11T13:18:44Z

qiita_pet/test/test_qiita_redbiom.py

+        response = self.post('/redbiom/', post_args)
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success',
+               'message': ('Not a valid search: "4353076", are you sure this '


cause it's not a stem ...

antgonza · 2017-05-11T13:20:42Z

qiita_pet/test/test_qiita_redbiom.py

+
+    def test_post_observations(self):
+        post_args = {
+            'search': ('4479944'),


you are right but they don't hurt or aren't flake8 complaint ... so?

antgonza · 2017-05-11T13:21:28Z

qiita_pet/test/test_qiita_redbiom.py

+        response = self.post('/redbiom/', post_args)
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success',
+               'message': ('Not a valid search: "4353076", are you sure this '


also not a stem ... I guess that it will become valid if a metadata category or value is 4353076, @wasade?

antgonza · 2017-05-11T13:23:33Z

scripts/qiita-test-install

@@ -395,6 +430,8 @@ def main():
        ipython_running = False
        extra_info = ('IPython test failed, perhaps due to an old MOI '
                      'version, please review')
+
+    print qiita_config_header


it's actually needed so it's displayed, see line https://github.com/biocore/qiita/pull/2118/files#diff-bb7154348182dace785aedbad03c3a2bL341

coveralls · 2017-05-11T14:06:36Z

Coverage decreased (-0.03%) to 91.949% when pulling f886d32 on antgonza:redbiom-ing into eb8863b on biocore:redbiom.

josenavas

Only a couple of small comments regarding JS library imports.,

josenavas · 2017-05-11T15:23:47Z

qiita_pet/handlers/qiita_redbiom.py

+
+        try:
+            df = redbiom.summarize.contexts()
+        except ConnectionError:


Ok, just wanted to make sure that this was the desired behavior.

josenavas · 2017-05-11T15:28:27Z

qiita_pet/static/js/qiita.js

@@ -117,3 +117,90 @@ function show_hide_process_list() {
    $("#qiita-processing").hide();
  }
 }
+


josenavas · 2017-05-11T15:30:39Z

qiita_pet/templates/redbiom.html

+<script type="text/javascript" src="{% raw qiita_config.portal_dir %}/static/js/sharing.js"></script>
+<script type="text/javascript">
+  $(document).ready(function() {
+    moi.init(null, window.location.host + '{% raw qiita_config.portal_dir %}/study/list/socket/', function(){}, error, error);


oh - thanks!

josenavas · 2017-05-11T15:31:19Z

qiita_pet/templates/sitebase.html

    <script src="{% raw qiita_config.portal_dir %}/static/js/qiita.js"></script>

+    <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>


This one is added twice (see line 49)

josenavas · 2017-05-11T15:33:38Z

qiita_pet/templates/redbiom.html

+{% extends sitebase.html %}
+
+{%block head%}
+<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/select2.min.css" type="text/css">


Just checked - select2.min.js it is added in sitebase.html but the css is not. I would suggest removing them from here and adding the css in the sitebase.html file. Since the JS is added there, somewhere in the code it is expected to be available but currently is not, which I can generate some problems down the line.

On the other hand, sharing.js is ok to leave here since it is only used here.

josenavas · 2017-05-11T15:37:17Z

qiita_pet/test/test_qiita_redbiom.py

+        response = self.post('/redbiom/', post_args)
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success',
+               'message': ('Not a valid search: "4353076", are you sure this '


In order to allow this to move forward, can this be added as a TODO item (even if it is only a discussion)? I don't understand why a number will not be a valid stem, or why searching over numerical values is not allowed. However, I don't want to block this PR for this discussion.

antgonza

thanks, changes soon!

antgonza · 2017-05-11T16:03:24Z

qiita_pet/templates/redbiom.html

+{% extends sitebase.html %}
+
+{%block head%}
+<link rel="stylesheet" href="{% raw qiita_config.portal_dir %}/static/vendor/css/select2.min.css" type="text/css">


k, removing all duplicated imports.

antgonza · 2017-05-11T16:05:59Z

qiita_pet/templates/sitebase.html

    <script src="{% raw qiita_config.portal_dir %}/static/js/qiita.js"></script>

+    <script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>


antgonza · 2017-05-11T16:06:43Z

qiita_pet/test/test_qiita_redbiom.py

+        response = self.post('/redbiom/', post_args)
+        self.assertEqual(response.code, 200)
+        exp = {'status': 'success',
+               'message': ('Not a valid search: "4353076", are you sure this '


k, will do, now numerical values are fine but have to be inclosed in a where, like where age_cat > 40

coveralls · 2017-05-11T16:24:34Z

Coverage decreased (-0.02%) to 91.958% when pulling 6e7cb7e on antgonza:redbiom-ing into eb8863b on biocore:redbiom.

antgonza added 23 commits April 26, 2017 09:18

installing redbiom

06bc8b2

classifiers=classifiers ??

41f0fcd

one of those days!

574c538

init commit

4210a61

Merge branch 'master' of https://github.com/biocore/qiita into redbio…

2c194fe

…m-ing

apt redis

36c41bf

redis-server &

8a7e9b7

redis-server

a23c360

Merge branch 'master' of https://github.com/biocore/qiita into redbio…

a870b3c

…m-ing

adding redbiom tests

acda0d0

redbiom setup.py

0e72f2a

redbiom #egg

a03f1cd

ready for test env

07fb481

Merge branch 'redbiom' of https://github.com/biocore/qiita into redbi…

0e56fa0

…om-ing

should fix tests

2da0aaf

redis 7777 &

c2a844b

before script redis-server

f1840f7

sudo: required

0ac26f1

adding more tests and REDBIOM_HOST

27d9968

rm redbiom from conf

e2bcaf9

retriving artifact info via SQL

369628a

retriving info from preps

cc5afbb

creating redbiom context

9bd1166

antgonza changed the title ~~WIP: redbiom-ing~~ Let's get redbiom-ing May 7, 2017

adding total of samples

28a9902

rm button when not logged

17e0780

wasade reviewed May 9, 2017

View reviewed changes

antgonza commented May 9, 2017

View reviewed changes

antgonza added 6 commits May 9, 2017 06:35

addressing @wasade initial comments

d378518

new gui + search on categories

16fc478

adding a connection error message

e41cdb4

request -> requests

babbede

rm query from connection error

0fc122b

changing callback placing

d46392e

josenavas suggested changes May 10, 2017

View reviewed changes

antgonza commented May 11, 2017

View reviewed changes

antgonza added 2 commits May 11, 2017 07:24

addressing @josenavas comments

c64a019

flake8

f886d32

josenavas suggested changes May 11, 2017

View reviewed changes

antgonza commented May 11, 2017

View reviewed changes

rm duplicated js imports

6e7cb7e

josenavas approved these changes May 11, 2017

View reviewed changes

wasade merged commit 5dc2b40 into qiita-spots:redbiom May 11, 2017

antgonza mentioned this pull request May 12, 2017

Adding Redbiom to master #2131

Closed

9 tasks

		<script src="{% raw qiita_config.portal_dir %}/static/js/qiita.js"></script>

		<script src="{% raw qiita_config.portal_dir %}/static/vendor/js/moi.js"></script>

Let's get redbiom-ing #2118

Let's get redbiom-ing #2118

Conversation

antgonza commented Apr 26, 2017

coveralls commented May 7, 2017

antgonza commented May 7, 2017

coveralls commented May 7, 2017

coveralls commented May 7, 2017

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coveralls commented May 10, 2017

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antgonza May 11, 2017 • edited Loading

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antgonza May 11, 2017 •

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